I can't explain why it might happen. I make a copy of each of my photos and documents before uploading to Ancestry. I have not had any lost yet. I did have all of the default photos on Ancestry.com disconnected one time when I had a problem with the sync feature of FTM. I'm still finding those since there were thousands of them affected. The programmers asked me for some details and logs of what I had done, though I never heard any more from them, other than "that shouldn't have happened and we will try to make sure it doesn't happen again."
If you are not already saving your photos and documents in a backup location, now might be a good time to start. :)